Yes, the cover installed with the molle panels without any mods. I installed all the molle panels myself and let the shop I bought the cover at install it. The front molle panel is pretty useless though.
I think you’d have to remove it. I installed the molle panels myself but had the cover installed. The panels install behind the bed rails and are pretty much flush with them. You use some of the bed rail screws for the installation. You’ll also have to drill a couple of holes in the bed.